ArticleRice (New York, N.Y.)2021
OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species.
Article in Rice (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 35 citations in OpenAlex.
- Whole-Genome Variants Resource of 144 Oryza rufipogon Accessions.Scientific data · 2026Article
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- ShiNyP: Unlocking SNP-Based Population Genetics-AI-Assisted Platform for Rapid and Interactive Visual Exploration.Molecular biology and evolution · 2025Article
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.bioRxiv : the preprint server for biology · 2025Article
- Evolution and diversification of the momilactone biosynthetic gene cluster in the genus Oryza.The New phytologist · 2025Article
- Usage of wildBreeding science · 2025Article
- African Cultivated, Wild and Weedy Rice (Biology · 2024Review
- Oryza CLIMtools: A genome-environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits.Plant communications · 2024Article
- Oryza CLIMtools: A Genome-Environment Association Resource Reveals Adaptive Roles for Heterotrimeric G Proteins in the Regulation of Rice Agronomic Traits.bioRxiv : the preprint server for biology · 2023Article
- A de novo evolved gene contributes to rice grain shape difference between indica and japonica.Nature communications · 2023Article
- Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms.International journal of molecular sciences · 2023Review
- Adaptation to high latitudes through a novel allele of Hd3a strongly promoting heading date in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Endophytic bacterial communities in wild rice (Frontiers in plant science · 2023Article
- Measurements of Antibacterial Activity of Seed Crude Extracts in Cultivated Rice and Wild Oryza Species.Rice (New York, N.Y.) · 2022Article
- Rice OsUBR7 modulates plant height by regulating histone H2B monoubiquitination and cell proliferation.Plant communications · 2022Article
- The first long-read nuclear genome assembly of Oryza australiensis, a wild rice from northern Australia.Scientific reports · 2022Article
- Collection, preservation and distribution ofBreeding science · 2021Article
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Authors and funding
20 authors at 7 institutions in 3 countries.
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Abstract
backgroundOryzaGenome ( http://viewer.shigen.info/oryzagenome21detail/index.xhtml ), a feature within Oryzabase ( https://shigen.nig.ac.jp/rice/oryzabase/ ), is a genomic database for wild Oryza species that provides comparative and evolutionary genomics approaches for the rice research community.
resultsHere we release OryzaGenome2.1, the first major update of OryzaGenome. The main feature in this version is the inclusion of newly sequenced genotypes and their meta-information, giving a total of 217 accessions of 19 wild Oryza species (O. rufipogon, O. barthii, O. longistaminata, O. meridionalis, O. glumaepatula, O. punctata, O. minuta, O. officinalis, O. rhizomatis, O. eichingeri, O. latifolia, O. alta, O. grandiglumis, O. australiensis, O. brachyantha, O. granulata, O. meyeriana, O. ridleyi, and O. longiglumis). These 19 wild species belong to 9 genome types (AA, BB, CC, BBCC, CCDD, EE, FF, GG, and HHJJ), representing wide genomic diversity in the genus. Using the genotype information, we analyzed the genome diversity of Oryza species. Other features of OryzaGenome facilitate the use of information on single nucleotide polymorphisms (SNPs) between O. sativa and its wild progenitor O. rufipogon in rice research, including breeding as well as basic science. For example, we provide Variant Call Format (VCF) files for genome-wide SNPs of 33 O. rufipogon accessions against the O. sativa reference genome, IRGSP1.0. In addition, we provide a new SNP Effect Table function, allowing users to identify SNPs or small insertion/deletion polymorphisms in the 33 O. rufipogon accessions and to search for the effect of these polymorphisms on protein function if they reside in the coding region (e.g., are missense or nonsense mutations). Furthermore, the SNP Viewer for 446 O. rufipogon accessions was updated by implementing new tracks for possible selective sweep regions and highly mutated regions that were potentially exposed to selective pressures during the process of domestication.
conclusionOryzaGenome2.1 focuses on comparative genomic analysis of diverse wild Oryza accessions collected around the world and on the development of resources to speed up the identification of critical trait-related genes, especially from O. rufipogon. It aims to promote the use of genotype information from wild accessions in rice breeding and potential future crop improvements. Diverse genotypes will be a key resource for evolutionary studies in Oryza, including polyploid biology.
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